View from ice cave on Ellesmere Island, Canada, towards the Arctic ocean and the north pole. Photograph: Alexandra Kobalenko/Getty

In a unique experiment, The Guardian published online the full manuscript of its major investigation into the climate science emails stolen from the University of East Anglia, which revealed apparent attempts to cover up flawed data; moves to prevent access to climate data; and to keep research from climate sceptics out of the scientific literature.

As well as including new information about the emails, we allowed web users to annotate the manuscript to help us in our aim of creating the definitive account of the controversy. This was an attempt at a collaborative route to getting at the truth.

We hoped to approach that complete account by harnessing the expertise of people with a special knowledge of, or information about, the emails. We wanted the protagonists on all sides of the debate to be involved, as well as people with expertise about the events and the science being described or more generally about the ethics of science. The only conditions are the comments abide by our community guidelines and add to the total knowledge or understanding of the events.

The annotations - and the real name of the commenter - were added to the manuscript, initially in private. The most insightful comments were then added to a public version of the manuscript. We hoped the process will be a form of peer review.

Is the science of climate change fatally flawed by the climategate revelations? Absolutely not. Nothing uncovered in the emails destroys the argument that humans are warming the planet.

None of the 1,073 emails plus 3,587 files containing documents, raw data and ­computer code upsets the 200-year-old science behind the "greenhouse effect" of gases such as carbon dioxide, which traps solar heat and warms the atmosphere. Nothing changes the fact that carbon dioxide is accumulating in the atmosphere thanks to human emissions from burning carbon-based fuels such as coal and oil. Nor the calculations by physicists that for every square metre of the Earth's surface, 1.6 watts more energy enters the atmosphere than leaves it.

These are not statistical artefacts or the result of scientists cherry-picking data. Equally, many of the most widely ­publicised claims from sceptics about the emails are demonstrably unfounded. There is no conspiracy to "hide the decline" in temperatures. Nor that a lack of warming in the data is a "travesty" – still less of attempts to fix the data.

But, within the narrower confines of assembling a reliable history of global ­temperature, the emails have done significant damage to the credibility of scientists. They show that in their desire to give the world a clear message that humans are ­heating the planet, a group of scientists cut corners and played down uncertainties in their calculations. Their opponents charge that they then covered their tracks by being secretive with data and suppressing dissent.

The long-standing critic of the IPCC process Roger Pielke Snr insists: "There are major problems with the accuracy of the surface temperature data." Jones and his colleagues know about the problems, he says. They make numerous adjustments to cope with them. "I do not question their sincerity," says Pielke. But "where they have failed is in preventing, in their leadership position, a proper scientific debate of the issues that we and others have raised." Such views were only heard on the scientific fringe before last November. They are more prominent today.

Part of the problem is secrecy in ­science. Judy Curry, a climatologist at the Georgia Institute of Technology who has been ­trying to make peace between her ­colleagues and the sceptics, says the various data sets connected to the famous "hockey stick" temperature graph and Phil Jones's thermometer data sets "stand out as lacking transparency".

Science is too much of a closed shop, she says. Outsiders need to be let into the ivory towers for the good of science itself. "Einstein didn't start his career at Princeton, but rather at a post office." Bring on the bloggers. Maybe there's an Einstein among them.

There is evidence in the emails that some at the Climatic Research Unit wanted to delete files rather than hand them over – though it is not clear if there were any deliberate deletions.

Probably no one anticipated that a law intended to unwrap state secrets might end up freeing data from scientists' computers. But the science community now urgently needs to figure out how to respond to this altered landscape.

The need to open up science is made all the greater by the question raised in the emails about the "gold standard", the peer review system. In many fields of research, peer review creates serious conflicts of interest in which, as the emails have revealed, senior researchers can act in a way that could have the effect of blackballing the research papers of their critics. The dangers are all the greater when, again as the emails show, the conventions of anonymity in peer review are not rigorously upheld.

Finally, "climategate" raises questions about the IPCC report-writing process, in which many of the emailers have been involved. Governments set up the IPCC 20 years ago to get scientists to speak with one voice on climate change. But often there is no clear consensus. Scientists are trained to disagree

The drive for consensus at the IPCC has created pressure to keep the message simple and for scientists who had a problem with that to keep quiet. Some shut up. Others bend their results or curtailed their researches to fit the prevailing view, arguably slowing down the process of scientific discovery. Others still react with anger to such requests and ended up among the outright sceptics. Such tensions are clear in dozens of the CRU emails.

Healing those divides may require an end to the IPCC in its present form. Jones's colleague at CRU Dr Mike Hulme is among those who suggests that the IPCC "has run its course". He says that "through its structural tendency to politicise climate change science [it] has perhaps helped to foster a more authoritarian and exclusive form of knowledge production – just at a time when globalising and wired cosmopolitan culture is demanding of science something much more open and inclusive."

Pielke in December criticised the "broad goal of the leadership of the IPCC process to control what science the policymakers receive." The emails expose that tendency. But the trouble is that the IPCC was set up by governments to do precisely that. The email hacking saga is a crisis for the IPCC process as a whole. But it also raises important questions about what we want of our scientists.

"Climate scientists will have to work harder to earn the warranted trust of the public – and maybe that is no bad thing," says Hulme. While science gets its house in order, we need some perspective. In the midst of a cold winter it may be hard to convince ourselves, but the world is still warming. Humanity is still to blame. And we still, urgently, need to do something about it.

Annotations

The text below consists of invited comments made on the Climate wars articles. They can be accessed in the main body of the article by clicking on the text to which they refer, which is highlighted in yellow.

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Read the full manuscript of the Guardian's major investigation into the climate science emails stolen from the University of East Anglia and send in your own annotations to create the definitive account of the controversy